How can I segment brain tissue with SPM without the GUI?

Question

We're trying to segment brain tissue types with SPM, and it is nearly impossible to find out online how to call its underlying matlab functions without using the GUI.

Some resources I found which did not help:

• SPM Manual
• SPM Book on Wikibooks

Answer 1

My colleague showed me how to call spm functions if you know how to do them in the gui. Go to the GUI and select save script from the menu. This results in the following code in two seperate files for segmentation:

job.m

matlabbatch{1}.spm.spatial.preproc.channel.vols = {'c:\test.nii,1'};
matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{1}.spm.spatial.preproc.channel.write = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm = {'C:\Program Files\spm12\tpm\TPM.nii,1'};
matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {'C:\Program Files\spm12\tpm\TPM.nii,2'};
matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {'C:\Program Files\spm12\tpm\TPM.nii,3'};
matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {'C:\Program Files\spm12\tpm\TPM.nii,4'};
matlabbatch{1}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{1}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {'C:\Program Files\spm12\tpm\TPM.nii,5'};
matlabbatch{1}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{1}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {'C:\Program Files\spm12\tpm\TPM.nii,6'};
matlabbatch{1}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{1}.spm.spatial.preproc.warp.write = [0 0];

runjob.m

nrun = 1;
jobfile = {'c:\job.m'};
jobs = repmat(jobfile, 1, nrun);
inputs = cell(0, nrun);
for crun = 1:nrun
end
spm('defaults', 'FMRI');
spm_jobman('run', jobs, inputs{:});

You can have a script edit the job.m file and then run the job.m file.